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Bodke S, Joshi N, Alavala RR, Suares D. In silico exploration of CB2 receptor agonist in the management of neuroinflammatory conditions by pharmacophore modeling. Comput Biol Chem 2024; 110:108049. [PMID: 38507844 DOI: 10.1016/j.compbiolchem.2024.108049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
Endocannabinoid system plays a pivotal role in controlling neuroinflammation, and modulating this system may not only aid in managing symptoms of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Epilepsy, Central and Peripheral neuropathic pain, but also, have the potential to target these diseases at an early-stage. In the present study, six different pharmacophore hypotheses were generated from Cannabidiol (CBD)-Cannabinoid Receptor subtype-2 (CB2) and then Zinc database was screened for identification of hit molecules. Identified 215 hit molecules were subjected to preliminary screening with ADMET and drug likeness properties, and about 48 molecules were found with no violations and toxicity properties. In molecular docking studies, six compounds showed better binding energy than CBD and β-caryophyllene (known inhibitor of CB2). These six molecules were designated as leads and subjected to re-docking with glide tool and Lead1 (ZINC000078815430) showed docking score of -9.877 kcal/mol, whereas CBD and β-caryophyllene showed score of -9.664 and -8.499 kcal/mol, respectively. Lead1 and CBD were evaluated for stability studies with Desmond tool by molecular dynamic simulation studies. Lead1 showed better stability than CBD in all studied parameters such as RMSD, RMSF, SSE, Rg, SASA, etc. In MM-GBSA free energy calculations, ΔGbinding energy of CB2-CBD complex and CB2-Lead1 were found to be -103.13±11.19 and -107.94±5.42 kcal/mol, respectively. Six lead molecules stated in the study hold promise with respect to CBD agonistic activity for treating and/or managing chronic conditions and can be explored as an alternative for early-stage cure, which has not yet been experimentally explored.
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Affiliation(s)
- Shlok Bodke
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai 400056, India
| | - Nachiket Joshi
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai 400056, India
| | - Rajasekhar Reddy Alavala
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai 400056, India.
| | - Divya Suares
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai 400056, India.
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2
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Wanas AS, Radwan MM, Marzouk AA, Elkaeed EB, Alsfouk BA, Mostafa AE, Eissa IH, Metwaly AM, ElSohly MA. Isolation and in silico investigation of cannflavins from Cannabis sativa leaves as potential anti-SARS-CoV-2 agents targeting the Papain-Like Protease. Nat Prod Res 2023:1-14. [PMID: 38100380 DOI: 10.1080/14786419.2023.2294111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
This study aimed to isolate and identify three prenylflavonoids (cannflavin A, B, and C) from Cannabis sativa leaves using different chromatographic techniques. The potential of the isolated compounds against SARS-CoV-2 was suggested through several in silico analysis. Structural similarity studies against nine co-crystallized ligands of SARS-CoV-2's proteins indicated the similarities of the isolated cannflavins with the SARS-CoV-2 Papain-Like Protease (PLP) ligand, Y95. Then, flexible allignment study confirmed this similarity. Docking experiments showed successful binding of all cannflavins within the active pocket of PLP, with energies comparable to Y95. Among them, cannflavin A demonstrated the most similar binding mode, while cannflavin C exhibited the best energy. Molecular dynamics (MD) simulations and MM-GPSA confirmed the accurate binding of cannflavin A to the PLP. In silico ADMET studies indicated favourable drug-like properties for all three compounds, suggesting their potential as anti-SARS-CoV-2 agents. Further In vitro and In vivo investigations are necessary to validate these findings and establish their efficacy and safety profiles.
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Affiliation(s)
- Amira S Wanas
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mohamed M Radwan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Adel A Marzouk
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Bshra A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahmad E Mostafa
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed M Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Mahmoud A ElSohly
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University, Mississippi, USA
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3
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Imanpour A, Kolahi Azar H, Makarem D, Nematollahi Z, Nahavandi R, Rostami M, Beheshtizadeh N. In silico engineering and simulation of RNA interferences nanoplatforms for osteoporosis treating and bone healing promoting. Sci Rep 2023; 13:18185. [PMID: 37875547 PMCID: PMC10598124 DOI: 10.1038/s41598-023-45183-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Osteoporosis is a bone condition characterized by reduced bone mineral density (BMD), poor bone microarchitecture/mineralization, and/or diminished bone strength. This asymptomatic disorder typically goes untreated until it presents as a low-trauma fracture of the hip, spine, proximal humerus, pelvis, and/or wrist, requiring surgery. Utilizing RNA interference (RNAi) may be accomplished in a number of ways, one of which is by the use of very tiny RNA molecules called microRNAs (miRNAs) and small interfering RNAs (siRNAs). Several kinds of antagomirs and siRNAs are now being developed to prevent the detrimental effects of miRNAs. The goal of this study is to find new antagonists for miRNAs and siRNAs that target multiple genes in order to reduce osteoporosis and promote bone repair. Also, choosing the optimum nanocarriers to deliver these RNAis appropriately to the body could lighten up the research road. In this context, we employed gene ontology analysis to search across multiple datasets. Following data analysis, a systems biology approach was used to process it. A molecular dynamics (MD) simulation was used to explore the possibility of incorporating the suggested siRNAs and miRNA antagonists into polymeric bioresponsive nanocarriers for delivery purposes. Among the three nanocarriers tested [polyethylene glycol (PEG), polyethylenimine (PEI), and PEG-PEI copolymer], MD simulations show that the integration of PEG-PEI with has-mIR-146a-5p is the most stable (total energy = -372.84 kJ/mol, Gyration radius = 2.1084 nm), whereas PEI is an appropriate delivery carrier for has-mIR-7155. The findings of the systems biology and MD simulations indicate that the proposed RNAis might be given through bioresponsive nanocarriers to accelerate bone repair and osteoporosis treatment.
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Affiliation(s)
- Aylar Imanpour
- Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hanieh Kolahi Azar
- Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Pathology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dorna Makarem
- Escuela Tecnica Superior de Ingenieros de Telecomunicacion, Politecnica de Madrid, Madrid, Spain
| | - Zeinab Nematollahi
- UCL Department of Nanotechnology, Division of Surgery and Interventional Science, University College London, London, UK
| | - Reza Nahavandi
- Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Biochemical and Pharmaceutical Engineering, School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, 11155-4563, Iran
| | - Mohammadreza Rostami
- Food Science and Nutrition Group (FSAN), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Division of Food Safety and Hygiene, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Beheshtizadeh
- Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Vasquez R, Batista L, Cuya T. Computational Study on the Enzyme-Ligand Relationship between Cannabis Phytochemicals and Human Acetylcholinesterase: Implications in Alzheimer's Disease. J Phys Chem B 2023; 127:8780-8795. [PMID: 37815196 DOI: 10.1021/acs.jpcb.3c04315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Cannabis has shown promise in treating various neurological disorders, including Alzheimer's disease (AD). AD is a devastating neurodegenerative disorder that affects millions of people worldwide. Current treatments for AD are limited and are not very effective. This study investigated the enzyme-ligand relationship between nine active components of cannabis and human acetylcholinesterase (HuAChE) enzyme, which is significant in AD. Specifically, computational methods such as quantum mechanics, molecular docking, molecular dynamics, and free energy calculations were used to identify the cannabis phytochemicals with the highest HuAChE affinity and to understand the specific binding mechanisms involved. Our results showed that cannabichromene and cannabigerol were the cannabis phytochemicals with the highest affinity for HuAChE, with cannabichromene exhibiting the greatest binding energy. However, both substances showed lower affinity than that of the pharmaceutical drug donepezil. This study suggests that cannabichromene has a specific affinity for the peripheral anionic site (PAS) and acyl-binding pocket (ABP), while cannabigerol predominantly binds to PAS. Also, it was found that cannabichromene has a specific affinity for PAS and ABP, while cannabigerol predominantly binds to PAS. Our findings suggest that cannabichromene and cannabigerol are potential therapeutic agents, but further research is needed to validate their effectiveness. The specific binding mechanisms identified may also provide helpful information for the design of more effective cannabis-based drugs. Overall, this study provides valuable insights into the potential of cannabis-based drugs for treating neurological diseases.
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Affiliation(s)
- Roxanne Vasquez
- Faculty of Technology, Department of Chemistry and Environment, University of the State of Rio de Janeiro, Resende, Rio de Janeiro 27537-000, Brazil
| | - Leonardo Batista
- Faculty of Technology, Department of Chemistry and Environment, University of the State of Rio de Janeiro, Resende, Rio de Janeiro 27537-000, Brazil
| | - Teobaldo Cuya
- Faculty of Technology, Department of Mathematics, Physics and Computation, University of the State of Rio de Janeiro, Resende, Rio de Janeiro 27537-000, Brazil
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5
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Zhang Y, Liu X, Chen J. Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. J Chem Inf Model 2022; 62:4523-4536. [PMID: 36083825 PMCID: PMC9910785 DOI: 10.1021/acs.jcim.2c00974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks and are now recognized to often remain highly dynamic even in specific interactions and assemblies. Accurate description of these dynamic interactions is extremely challenging using atomistic simulations because of the prohibitive computational cost. Efficient coarse-grained approaches could offer an effective solution to overcome this bottleneck if they could provide an accurate description of key local and global properties of IDPs in both unbound and bound states. The recently developed hybrid-resolution (HyRes) protein model has been shown to be capable of providing a semiquantitative description of the secondary structure propensities of IDPs. Here, we show that greatly improved description of global structures and transient interactions can be achieved by introducing a solvent-accessible surface area-based implicit solvent term followed by reoptimization of effective interaction strengths. The new model, termed HyRes II, can semiquantitatively reproduce a wide range of local and global structural properties of a set of IDPs of various lengths and complexities. It can also distinguish the level of compaction between folded proteins and IDPs. In particular, applied to the disordered N-terminal transactivation domain (TAD) of tumor suppressor p53, HyRes II is able to recapitulate various nontrivial structural properties compared to experimental results, some of them to a level of accuracy that is almost comparable to results from atomistic explicit solvent simulations. Furthermore, we demonstrate that HyRes II can be used to simulate the dynamic interactions of TAD with the DNA-binding domain of p53, generating structural ensembles that are highly consistent with existing NMR data. We anticipate that HyRes II will provide an efficient and relatively reliable tool toward accurate coarse-grained simulations of dynamic protein interactions.
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Affiliation(s)
- Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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6
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Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds. Blood Adv 2022; 6:4015-4027. [PMID: 35561308 PMCID: PMC9278297 DOI: 10.1182/bloodadvances.2022006977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022] Open
Abstract
Fibrin polymerization involves thrombin-mediated exposure of knobs on one monomer that bind to holes available on another, leading to the formation of fibers. In silico evidence has suggested that the classical A:a knob-hole interaction is enhanced by surrounding residues not directly involved in the binding pocket of hole a, via noncovalent interactions with knob A. We assessed the importance of extended knob-hole interactions by performing biochemical, biophysical, and in silico modeling studies on recombinant human fibrinogen variants with mutations at residues responsible for the extended interactions. Three single fibrinogen variants, γD297N, γE323Q, and γK356Q, and a triple variant γDEK (γD297N/γE323Q/γK356Q) were produced in a CHO (Chinese Hamster Ovary) cell expression system. Longitudinal protofibril growth probed by atomic force microscopy was disrupted for γD297N and enhanced for the γK356Q mutation. Initial polymerization rates were reduced for all variants in turbidimetric studies. Laser scanning confocal microscopy showed that γDEK and γE323Q produced denser clots, whereas γD297N and γK356Q were similar to wild type. Scanning electron microscopy and light scattering studies showed that fiber thickness and protofibril packing of the fibers were reduced for all variants. Clot viscoelastic analysis showed that only γDEK was more readily deformable. In silico modeling suggested that most variants displayed only slip-bond dissociation kinetics compared with biphasic catch-slip kinetics characteristics of wild type. These data provide new evidence for the role of extended interactions in supporting the classical knob-hole bonds involving catch-slip behavior in fibrin formation, clot structure, and clot mechanics.
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7
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Skokowa J, Hernandez Alvarez B, Coles M, Ritter M, Nasri M, Haaf J, Aghaallaei N, Xu Y, Mir P, Krahl AC, Rogers KW, Maksymenko K, Bajoghli B, Welte K, Lupas AN, Müller P, ElGamacy M. A topological refactoring design strategy yields highly stable granulopoietic proteins. Nat Commun 2022; 13:2948. [PMID: 35618709 PMCID: PMC9135769 DOI: 10.1038/s41467-022-30157-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 04/19/2022] [Indexed: 11/09/2022] Open
Abstract
Protein therapeutics frequently face major challenges, including complicated production, instability, poor solubility, and aggregation. De novo protein design can readily address these challenges. Here, we demonstrate the utility of a topological refactoring strategy to design novel granulopoietic proteins starting from the granulocyte-colony stimulating factor (G-CSF) structure. We change a protein fold by rearranging the sequence and optimising it towards the new fold. Testing four designs, we obtain two that possess nanomolar activity, the most active of which is highly thermostable and protease-resistant, and matches its designed structure to atomic accuracy. While the designs possess starkly different sequence and structure from the native G-CSF, they show specific activity in differentiating primary human haematopoietic stem cells into mature neutrophils. The designs also show significant and specific activity in vivo. Our topological refactoring approach is largely independent of sequence or structural context, and is therefore applicable to a wide range of protein targets. Skokowa et al. reconstruct the fold of a granulopoietic cytokine, resulting in de novo, hyperstable, highly active proteins with therapeutic potential for treating several neutropenia disorders.
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Affiliation(s)
- Julia Skokowa
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany.
| | | | - Murray Coles
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Malte Ritter
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Masoud Nasri
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Jérémy Haaf
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Narges Aghaallaei
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Yun Xu
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Perihan Mir
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Ann-Christin Krahl
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Katherine W Rogers
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kateryna Maksymenko
- Max Planck Institute for Biology, 72076, Tübingen, Germany.,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany
| | - Baubak Bajoghli
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Karl Welte
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Mohammad ElGamacy
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany. .,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany. .,Heliopolis Biotechnology Ltd, Cambridge, CB24 9RX, UK. .,Max Planck Institute for Biology, 72076, Tübingen, Germany.
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8
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Developments in the diffusive gradients in thin-films technique for the speciation of oxyanions and platinum group elements in aquatic systems. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Nordquist EB, English CA, Clerico EM, Sherman W, Gierasch LM, Chen J. Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. PLoS Comput Biol 2021; 17:e1009567. [PMID: 34735438 PMCID: PMC8604352 DOI: 10.1371/journal.pcbi.1009567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/19/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences ("selective promiscuity"). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, binds to sequences containing three to five branched hydrophobic residues, although otherwise the specific amino acids can vary considerably. Several high-resolution structures of the substrate -binding domain (SBD) of DnaK bound to peptides reveal a highly conserved configuration of the bound substrate and further suggest that the substrate-binding cleft consists of five largely independent sites for interaction with five consecutive substrate residues. Importantly, both substrate backbone orientations (N- to C- and C- to N-) allow essentially the same backbone hydrogen-bonding and side-chain interactions with the chaperone. In order to rationalize these observations, we performed atomistic molecular dynamics simulations to sample the interactions of all 20 amino acid side chains in each of the five sites of the chaperone in the context of the conserved substrate backbone configurations. The resulting interaction energetics provide the basis set for deriving a predictive model that we call Paladin (Physics-based model of DnaK-Substrate Binding). Trained using available peptide array data, Paladin can distinguish binders and nonbinders of DnaK with accuracy comparable to existing predictors and further predicts the detailed configuration of the bound sequence. Tested using existing DnaK-peptide structures, Paladin correctly predicted the binding register in 10 out of 13 substrate sequences that bind in the N- to C- orientation, and the binding orientation in 16 out of 22 sequences. The physical basis of the Paladin model provides insight into the origins of how Hsp70s bind substrates with a balance of selectivity and promiscuity. The approach described here can be extended to other Hsp70s where extensive peptide array data is not available.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Charles A. English
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Impact, New York City, New York, United States of America
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Woody Sherman
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Roivant Sciences, Boston, Massachusetts, United States of America
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- * E-mail: (LMG); (JC)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- * E-mail: (LMG); (JC)
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10
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Sgrignani J, Cecchinato V, Fassi EMA, D'Agostino G, Garofalo M, Danelon G, Pedotti M, Simonelli L, Varani L, Grazioso G, Uguccioni M, Cavalli A. Systematic Development of Peptide Inhibitors Targeting the CXCL12/HMGB1 Interaction. J Med Chem 2021; 64:13439-13450. [PMID: 34510899 DOI: 10.1021/acs.jmedchem.1c00852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During inflammatory reactions, the production and release of chemotactic factors guide the recruitment of selective leukocyte subpopulations. The alarmin HMGB1 and the chemokine CXCL12, both released in the microenvironment, can form a heterocomplex, which exclusively acts on the chemokine receptor CXCR4, enhancing cell migration, and in some pathological conditions such as rheumatoid arthritis exacerbates the immune response. An excessive cell influx at the inflammatory site can be diminished by disrupting the heterocomplex. Here, we report the computationally driven identification of the first peptide (HBP08) binding HMGB1 and selectively inhibiting the activity of the CXCL12/HMGB1 heterocomplex. Furthermore, HBP08 binds HMGB1 with the highest affinity reported so far (Kd of 0.8 ± 0.4 μM). The identification of this peptide represents an important step toward the development of innovative pharmacological tools for the treatment of severe chronic inflammatory conditions characterized by an uncontrolled immune response.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Enrico M A Fassi
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Gianluca D'Agostino
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Maura Garofalo
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Gabriela Danelon
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090 Milan, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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11
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Patel KB, Kononova O, Cai S, Barsegov V, Parmar VS, Kumar R, Singh BR. Botulinum neurotoxin inhibitor binding dynamics and kinetics relevant for drug design. Biochim Biophys Acta Gen Subj 2021; 1865:129933. [PMID: 34023445 DOI: 10.1016/j.bbagen.2021.129933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A). METHODS In this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC. RESULTS Studies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site. CONCLUSION The NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT. GENERAL SIGNIFICANCE Insights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.
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Affiliation(s)
- Kruti B Patel
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Olga Kononova
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Valeri Barsegov
- Department of Chemistry and Biochemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Virinder S Parmar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA, USA; Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, MA, USA; Prime Bio Inc., Dartmouth, MA, USA.
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12
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Arsiccio A, Shea JE. Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. J Phys Chem B 2021; 125:5222-5232. [DOI: 10.1021/acs.jpcb.1c01694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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13
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Flügel K, Schmidt K, Mareczek L, Gäbe M, Hennig R, Thommes M. Impact of incorporated drugs on material properties of amorphous solid dispersions. Eur J Pharm Biopharm 2021; 159:88-98. [PMID: 33383170 DOI: 10.1016/j.ejpb.2020.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022]
Abstract
Formulation development of amorphous solid dispersions (ASD) still is challenging although several poorly water-soluble drugs have been marketed using this technique. During development of novel drugs, the selection of the preparation technique and polymer matrix is commonly performed for the certain drug via screening tools. However, if general trends regarding material properties are to be investigated, this approach is not beneficial, although often utilized in literature. The main component of the ASD usually is the polymer and thus it predominantly determines the material properties of the system. Therefore, to study the impact of different drugs and their drug loads on mechanical properties and wettability, three poorly soluble model drugs with drug loads ranging from 10% to 40% were incorporated into copovidone via hot-melt extrusion. The obtained extrudates were subsequently characterized regarding mechanical properties by applying diametral compression test and nanoindentation and the results were compared to the performance during tablet compression. Incorporation of all tested drugs resulted in a similar increase in brittleness of the ASDs, whereas the Young's modulus and hardness changed differently in dependence of the incorporated drug. These observations correlated well with the performance during tablet compression and it was concluded, that the brittleness seemed to be the predominant factor influencing the compression behavior of copovidone-based ASDs. Furthermore, the degree of water absorption and wettability was assessed by applying dynamic vapor sorption experiments and contact angle measurements. Here, the incorporated drugs impacted the contact angle to different degrees and a strong correlation between the contact angle and disintegration time was observable. These results highlight the importance of thorough characterization of the ASDs as it helps to predict their performance during tablet compression and thus facilitates the optimal selection of excipients.
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Affiliation(s)
- Karsten Flügel
- Faculty of Biochemical and Chemical Engineering, Laboratory of Solids Process Engineering, Technical University Dortmund, Emil-Figge-Str. 68, 44227 Dortmund, Germany; Department of Pharmaceutical Technologies, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Katharina Schmidt
- Department of Pharmaceutical Technologies, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Lena Mareczek
- Department of Pharmaceutical Technologies, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Michael Gäbe
- Department of Pharmaceutical Technologies, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Robert Hennig
- Department of Pharmaceutical Technologies, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Markus Thommes
- Faculty of Biochemical and Chemical Engineering, Laboratory of Solids Process Engineering, Technical University Dortmund, Emil-Figge-Str. 68, 44227 Dortmund, Germany.
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14
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Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Sci Rep 2020; 10:18211. [PMID: 33097750 PMCID: PMC7585447 DOI: 10.1038/s41598-020-75239-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.
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Affiliation(s)
- Nana Heilmann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Moritz Wolf
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Elaheh Sedghamiz
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Julia Setzler
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Brieg
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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15
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Singh A, Mishra A. Molecular dynamics simulation and free energy calculation studies of Coagulin L as dipeptidyl peptidase-4 inhibitor. J Biomol Struct Dyn 2020; 40:1128-1138. [PMID: 33078683 DOI: 10.1080/07391102.2020.1822917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Plant derived product can be used as other alternatives to currently used drugs for controlling chronic diseases like Diabetes mellitus. The potential of Coagulin L (a constituent of Withania coagulans) as dipeptidyl peptidase-4 (DPP-4) inhibitor was evaluated by molecular modelling study. It was observed that amino acid residues such as Glu205, Glu206, Tyr 547, His 740, and Try662 interacts with Coagulin L and Saxagliptin (a known DPP-4 inhibitor). Other nonbonded interactions of Coagulin L and Saxagliptin with DPP-4 binding residues were also found similar. The docking energy of Coagulin L was found to be -7.69 Kcal/mol whereas -8.44 kcal/mol was recorded for Saxagliptin. MD simulation study revealed stable binding throughout 100 ns simulation. RMSD plot of the complex was stabilized in 43 ns and remained stable during entire simulation(100 ns). RMSF plot of DPP-4 Coagulin L interaction showed major fluctuations at residue 246 and 766, however, Arg 125, Glu 205, Ser 209 and His 740 showed no major perturbations. Principal Component Analysis showed that important dynamics of the protein remain unchanged during entire simulation since the non-polar, van der waals, ionic interaction and solvation energy, altogether play important role in the complex stability. The molecular modelling study of DPP-4 with Coagulin L was an effort to establish correlation with traditional practices of Withania coagulans as antidiabetic agent in Indian subcontinent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Singh
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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16
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Kumar R, Maksudov F, Kononova O, Marx KA, Barsegov V, Singh BR. Botulinum Endopeptidase: SAXS Experiments and MD Simulations Reveal Extended Solution Structures That Account for Its Biochemical Properties. J Phys Chem B 2020; 124:5801-5812. [PMID: 32543194 DOI: 10.1021/acs.jpcb.0c02817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of antidotes against botulism requires understanding of the enzymatically active conformations of Botulinum neurotoxin serotype A (BoNT/A) light chain (LCA). We performed small angle X-ray scattering (SAXS) to characterize the solution structures of truncated light chain (tLCA). The 34-37 Å radius of gyration of tLCA was 1.5-times greater than the averaged 22-23-Å radius from the crystal structures. The bimodal distribution of interatomic distances P(r) indicated the two-domain tLCA structure with 129-133 Å size, and Kratky plots indicated the tLCA partial unfolding in the 25-37 °C temperature range. To interpret these data, we employed molecular dynamics simulations and machine learning. Excellent agreement between experimental and theoretical P(r) profiles helped to resolve conformational subpopulations of tLCA in solution. Partial unfolding of the C-terminal portion of tLCA (residues 339-425) results in formation of extended conformations with the larger globular domain (residues 2-298) and the smaller unstructured domain (339-425). The catalytic domain, buried 20 Å-deep inside the crystal structure, becomes accessible in extended solution conformations (8-9 Å deep). The C- and N-termini containing different functional sequence motifs are maximally separated in the extended conformations. Our results offer physical insights into the molecular basis of BoNT/A function and stress the importance of reversible unfolding-refolding transitions and hydrophobic interactions.
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Affiliation(s)
- Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, Massachusetts 02747, United States
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Olga Kononova
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, Massachusetts 02747, United States
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17
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The Dependence of Implicit Solvent Model Parameters and Electronic Absorption Spectra and Photoinduced Charge Transfer. Sci Rep 2020; 10:3713. [PMID: 32111955 PMCID: PMC7048810 DOI: 10.1038/s41598-020-60757-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/17/2020] [Indexed: 11/20/2022] Open
Abstract
In this work, the relationship between multiple solvent parameters and charge transfer index was analyzed by multi-factor multi-variate partial least squares regression (PLSR). The charge transfer of the molecule is visualized by the analysis of the excited state wave function. Hydrogen bond basicity and surface tension can significantly affect charge transfer by studying the solvation model parameters and charge transfer index. Finally, a method in which a solvent regulates charge transfer strength and migration length is proposed.
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18
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Guduru S, Singh ML, Pahari P. Thermodynamic distribution ratio model for PUREX major solutes. SEP SCI TECHNOL 2019. [DOI: 10.1080/01496395.2019.1569060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sreeshailam Guduru
- Computational Analysis Division, Bhabha Atomic Research Centre, Visakhapatnam, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mani Lal Singh
- Nuclear Recycle Board, Bhabha Atomic Research Centre, Trombay, India
| | - Poonam Pahari
- Computational Analysis Division, Bhabha Atomic Research Centre, Visakhapatnam, India
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19
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Chakravorty A, Gallicchio E, Alexov E. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J Comput Chem 2019; 40:1290-1304. [PMID: 30698861 PMCID: PMC6506848 DOI: 10.1002/jcc.25786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 11/06/2022]
Abstract
A novel grid-based method is presented, which in conjunction with a smooth Gaussian-based model of atoms, is used to compute molecular volume (MV) and surface area (MSA). The MV and MSA are essential for computing nonpolar component of free energies. The objective of our grid-based approach is to identify solute atom pairs that share overlapping volumes in space. Once completed, this information is used to construct a rooted tree using depth-first method to yield the final volume and SA by using the formulations of the Gaussian model described by Grant and Pickup (J. Phys Chem, 1995, 99, 3503). The method is designed to function uninterruptedly with the grid-based finite-difference method implemented in Delphi, a popular and open-source package used for solving the Poisson-Boltzmann equation (PBE). We demonstrate the time efficacy of the method while also validating its performance in terms of the effect of grid-resolution, positioning of the solute within the grid-map and accuracy in identification of overlapping atom pairs. We also explore and discuss different aspects of the Gaussian model with key emphasis on its physical meaningfulness. This development and its future release with the Delphi package are intended to provide a physically meaningful, fast, robust and comprehensive tool for MM/PBSA based free energy calculations. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Arghya Chakravorty
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634
| | | | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634
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20
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Sangiorgi N, Sangiorgi A, Tarterini F, Sanson A. Molecularly imprinted polypyrrole counter electrode for gel-state dye-sensitized solar cells. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Ortega M, Vilhena JG, Rubio-Pereda P, Serena PA, Pérez R. Assessing the Accuracy of Different Solvation Models To Describe Protein Adsorption. J Chem Theory Comput 2019; 15:2548-2560. [PMID: 30822382 DOI: 10.1021/acs.jctc.8b01060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In protein adsorption, the surrounding solvent has an important role in mediating protein-surface interactions. Therefore, it is of paramount importance that the solvent methods employed to model these kinds of processes are able to correctly capture the complex mechanisms occurring in the protein-water-surface interface. Here, we test the suitability of the two most popular implicit solvent methods based on the Generalized Born formalism to describe the adsorption process of the immunoglobulin G (IgG) on a hydrophobic graphene surface. Our results show that in both cases, IgG experiences an extreme and early (in less than 40 ns) unfolding as a result of the adsorption to the surface in contrast with previous experimental findings. A detailed energy decomposition analysis of explicit and implicit solvent simulations reveals that this discrepancy arises from the ill-characterization of two energy components in implicit solvent methods. These findings help to elucidate how implicit solvent models may be improved to accurately characterize the protein adsorption process.
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Affiliation(s)
| | - J G Vilhena
- Department of Physics , University of Basel , Klingelbergstrasse 82 , CH-4056 Basel , Switzerland
| | - Pamela Rubio-Pereda
- Instituto de Ciencia de Materiales de Madrid (ICMM) , CSIC , c/Sor Juana Ines de la Cruz 3 , E-28049 Madrid , Spain.,Centro de Investigación Científica y de Educación Superior de Ensenada 3918 , 22860 Ensenada , Baja California , Mexico
| | - P A Serena
- Instituto de Ciencia de Materiales de Madrid (ICMM) , CSIC , c/Sor Juana Ines de la Cruz 3 , E-28049 Madrid , Spain
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22
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Chekmarev SF. Alternation of phases of regular and irregular dynamics in protein folding. Phys Rev E 2019; 99:022412. [PMID: 30934237 DOI: 10.1103/physreve.99.022412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Indexed: 06/09/2023]
Abstract
The regularity of the dynamics in different phases of protein folding is investigated for a set of proteins which undergo a cooperative, two-state folding transition. To determine the degree of regularity of the dynamics, the fractal dimension of probability fluxes is calculated on the basis of simulated folding trajectories. It has been found that the phases of regular and irregular dynamics alternate as follows. In the initial (collapse) phase of folding, the dynamics are essentially regular. Then, as the protein comes to the basin of semicompact states that precedes the transition state, the dynamics become irregular. At the transition state, the dynamics are regularized again but become less regular when the nativelike states are explored. Depending on the specific conditions at which the protein folding was considered, some phases of the dynamics could not be well resolved, but no significant deviation from this general picture has been observed. The regularization of the dynamics at the transition state is discussed in relation to the recent studies of the Hamiltonian dynamics of small clusters, where both regular and chaotic dynamics were observed depending on the flatness of the energy surface at the transition state.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia and Physics Department, Novosibirsk State University, 630090 Novosibirsk, Russia
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23
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Steinbach PJ. Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model. J Phys Chem B 2018; 122:11355-11362. [PMID: 30230838 DOI: 10.1021/acs.jpcb.8b07264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A continuum solvent model based on screened Coulomb potentials has been simplified and parametrized to sample native-like structures in replica-exchange simulations of each of six different peptides and miniproteins. Low-energy, native, and non-native structures were used to iteratively refine 11 parameter values. The centroid of the largest cluster of structures sampled in simulations initiated from an extended conformation represents the predicted structure. The main-chain rms deviation of this prediction from the experimental structure was 0.47 Å for the 12-residue Trp-zip2, 0.86 Å for the 14-residue MBH12, 2.53 Å for the 17-residue U(1-17)T9D, 2.03 Å for the 20-residue BS1, 1.08 Å for the 20-residue Trp-cage, and 3.64 Å for the 35-residue villin headpiece subdomain HP35. The centroid of the sixth largest cluster sampled for HP35 deviated by 0.91 Å. The CHARMM22/CMAP force field was used, with an additional ψ torsion term for residues other than glycine and proline. Six parameters govern the dielectric response of the continuum solvent, and four values of surface tension approximate nonpolar effects. An atom's self-energy and interaction energies are screened independently, each depending on whether the atom is part of a charged group, a neutral hydrogen-bonding main-chain group, or any other neutral group. The parameters inferred result in strong main-chain hydrogen bonds, consistent with the view that protein folding is dominated by the formation of these bonds. (1,2) Conformations of MBH12 and BS1 were excluded from the energy-function refinement, suggesting the parameters, referred to as SCP18, are transferable. An efficient estimate of solvent-accessible surface area is also described.
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Affiliation(s)
- Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology , National Institutes of Health , Bethesda , Maryland 20892 , United States
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24
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Ranbhor R, Kumar A, Tendulkar A, Patel K, Ramakrishnan V, Durani S. IDeAS: automated design tool for hetero-chiral protein folds. Phys Biol 2018; 15:066005. [PMID: 29923499 DOI: 10.1088/1478-3975/aacdc3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporating D amino acids in the protein design alphabet can in principle multiply the design space by many orders of magnitude. All native proteins are polymers composed of L chiral amino acids. Practically limitless in diversity over amino acid sequences, protein structure is limited in folds and thus shapes, principally due to the poly L stereochemistry of their backbone. To diversify shapes, we introduced both L- and D α-amino acids as design alphabets to explore the possibility of generating novel folds, varied in chemical as well as stereo-chemical sequence. Now, to have stereochemically-defined proteins tuned chemically, we present the Inverse Design and Automation Software, IDeAS. Retro-fitting side chains on a backbone with L and D stereochemistry, the software demonstrate functional fits over stereo-chemically diverse folds in a range of applications of interest in protein design.
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Affiliation(s)
- Ranjit Ranbhor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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25
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Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds. Proc Natl Acad Sci U S A 2018; 115:8575-8580. [PMID: 30087181 DOI: 10.1073/pnas.1802576115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fibrin formation and mechanical stability are essential in thrombosis and hemostasis. To reveal how mechanical load impacts fibrin, we carried out optical trap-based single-molecule forced unbinding experiments. The strength of noncovalent A:a knob-hole bond stabilizing fibrin polymers first increases with tensile force (catch bonds) and then decreases with force when the force exceeds a critical value (slip bonds). To provide the structural basis of catch-slip-bond behavior, we analyzed crystal structures and performed molecular modeling of A:a knob-hole complex. The movable flap (residues γ295 to γ305) containing the weak calcium-binding site γ2 serves as a tension sensor. Flap dissociation from the B domain in the γ-nodule and translocation to knob 'A' triggers hole 'a' closure, resulting in the increase of binding affinity and prolonged bond lifetimes. The discovery of biphasic kinetics of knob-hole bond rupture is quantitatively explained by using a theory, formulated in terms of structural transitions in the binding pocket between the low-affinity (slip) and high-affinity (catch) states. We provide a general framework to understand the mechanical response of protein pairs capable of tension-induced remodeling of their association interface. Strengthening of the A:a knob-hole bonds at 30- to 40-pN forces might favor formation of nascent fibrin clots subject to hydrodynamic shear in vivo.
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26
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Zhmurov A, Protopopova AD, Litvinov RI, Zhukov P, Weisel JW, Barsegov V. Atomic Structural Models of Fibrin Oligomers. Structure 2018; 26:857-868.e4. [PMID: 29754827 PMCID: PMC6501597 DOI: 10.1016/j.str.2018.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/06/2018] [Accepted: 04/05/2018] [Indexed: 10/16/2022]
Abstract
The space-filling fibrin network is a major part of clots and thrombi formed in blood. Fibrin polymerization starts when fibrinogen, a plasma protein, is proteolytically converted to fibrin, which self-assembles to form double-stranded protofibrils. When reaching a critical length, these intermediate species aggregate laterally to transform into fibers arranged into branched fibrin network. We combined multiscale modeling in silico with atomic force microscopy (AFM) imaging to reconstruct complete atomic models of double-stranded fibrin protofibrils with γ-γ crosslinking, A:a and B:b knob-hole bonds, and αC regions-all important structural determinants not resolved crystallographically. Structures of fibrin oligomers and protofibrils containing up to 19 monomers were successfully validated by quantitative comparison with high-resolution AFM images. We characterized the protofibril twisting, bending, kinking, and reversibility of A:a knob-hole bonds, and calculated hydrodynamic parameters of fibrin oligomers. Atomic structures of protofibrils provide a basis to understand mechanisms of early stages of fibrin polymerization.
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Affiliation(s)
- Artem Zhmurov
- Moscow Institute of Physics & Technology, Dolgoprudny, Moscow Region 141700, Russian Federation; Sechenov University, Moscow 119991, Russian Federation
| | - Anna D Protopopova
- Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rustem I Litvinov
- Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Pavel Zhukov
- Moscow Institute of Physics & Technology, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - John W Weisel
- Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Valeri Barsegov
- Moscow Institute of Physics & Technology, Dolgoprudny, Moscow Region 141700, Russian Federation; Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.
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27
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Thanki K, Prajapati R, Sangamwar AT, Jain S. Long chain fatty acid conjugation remarkably decreases the aggregation induced toxicity of Amphotericin B. Int J Pharm 2018; 544:1-13. [DOI: 10.1016/j.ijpharm.2018.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 01/22/2023]
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Andryushchenko VA, Chekmarev SF. Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows. PLoS One 2017; 12:e0188659. [PMID: 29206845 PMCID: PMC5716548 DOI: 10.1371/journal.pone.0188659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 11/10/2017] [Indexed: 11/19/2022] Open
Abstract
Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence. Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows. Using molecular dynamics simulations, we study folding of another benchmark system—Trp-cage miniprotein, which has different content of secondary structure elements and mechanism of folding. Calculating the probability fluxes of transitions in a three-dimensional space of collective variables, we have found that similar to the SH3 domain, the structure functions of the second and third orders correspond to the Kolmogorov functions. The spatial distributions of the probability fluxes are self-similar with a fractal dimension, and the fractal index decreases toward the native state, indicating that the flow becomes more turbulent as the native state is approached. We also show that the process of folding can be viewed as Brownian diffusion in the space of probability fluxes. The diffusion coefficient plays a role of the key parameter that defines the structures functions, similar to the rate of dissipation of kinetic energy in hydrodynamic turbulence. The obtained results, first, show that the very complex dynamics of protein folding allows a simple characterization in terms of scaling and diffusion of probability fluxes, and, secondly, they suggest that the turbulence phenomena similar to hydrodynamic turbulence are not specific of folding of a particular protein but are common to protein folding.
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Affiliation(s)
- Vladimir A. Andryushchenko
- Institute of Thermophysics, SB RAS, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia
| | - Sergei F. Chekmarev
- Institute of Thermophysics, SB RAS, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
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29
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Jiang N, Bailey ME, Burke J, Ross JL, Dima RI. Modeling the effects of lattice defects on microtubule breaking and healing. Cytoskeleton (Hoboken) 2017; 74:3-17. [PMID: 27935245 DOI: 10.1002/cm.21346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 12/19/2022]
Abstract
Microtubule reorganization often results from the loss of polymer induced through breakage or active destruction by energy-using enzymes. Pre-existing defects in the microtubule lattice likely lower structural integrity and aid filament destruction. Using large-scale molecular simulations, we model diverse microtubule fragments under forces generated at specific positions to locally crush the filament. We show that lattices with 2% defects are crushed and severed by forces three times smaller than defect-free ones. We validate our results with direct comparisons of microtubule kinking angles during severing. We find a high statistical correlation between the angle distributions from experiments and simulations indicating that they sample the same population of structures. Our simulations also indicate that the mechanical environment of the filament affects breaking: local mechanical support inhibits healing after severing, especially in the case of filaments with defects. These results recall reports of microtubule healing after flow-induced bending and corroborate prior experimental studies that show severing is more likely at locations where microtubules crossover in networks. Our results shed new light on mechanisms underlying the ability of microtubules to be destroyed and healed in the cell, either by external forces or by severing enzymes wedging dimers apart. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
| | - Megan E Bailey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Jessica Burke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
| | - Jennifer L Ross
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts, 01003.,Department of Physics, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221
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30
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Minin KA, Zhmurov A, Marx KA, Purohit PK, Barsegov V. Dynamic Transition from α-Helices to β-Sheets in Polypeptide Coiled-Coil Motifs. J Am Chem Soc 2017; 139:16168-16177. [PMID: 29043794 DOI: 10.1021/jacs.7b06883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We carried out dynamic force manipulations in silico on a variety of coiled-coil protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their α-helical packing. When stretched along the superhelical axis, all superhelices show elastic, plastic, and inelastic elongation regimes and undergo a dynamic transition from the α-helices to the β-sheets, which marks the onset of plastic deformation. Using the Abeyaratne-Knowles formulation of phase transitions, we developed a new theoretical methodology to model mechanical and kinetic properties of protein coiled-coils under mechanical nonequilibrium conditions and to map out their energy landscapes. The theory was successfully validated by comparing the simulated and theoretical force-strain spectra. We derived the scaling laws for the elastic force and the force for α-to-β transition, which can be used to understand natural proteins' properties as well as to rationally design novel biomaterials of required mechanical strength with desired balance between stiffness and plasticity.
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Affiliation(s)
- Kirill A Minin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia
| | - Artem Zhmurov
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Valeri Barsegov
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia.,Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
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31
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Gowdy J, Batchelor M, Neelov I, Paci E. Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes? J Phys Chem B 2017; 121:9518-9525. [DOI: 10.1021/acs.jpcb.7b07075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James Gowdy
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, U.K
| | - Matthew Batchelor
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, U.K
| | - Igor Neelov
- Institute
of Macromolecular Compounds of Russian Academy of Sciences, St. Petersburg, Russia
| | - Emanuele Paci
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, U.K
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32
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Andryushchenko VA, Chekmarev SF. Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes. J Biol Phys 2017; 43:565-583. [PMID: 28983809 DOI: 10.1007/s10867-017-9470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/01/2017] [Indexed: 11/25/2022] Open
Abstract
Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear. To gain insight into this issue, we employ a recently proposed hydrodynamic description of protein folding, in which the process of folding is considered as a motion of a "folding fluid" (Chekmarev et al., Phys. Rev. Lett. 100(1), 018107 2008). Using molecular dynamics simulations, we determine the field of probability fluxes of transitions in a space of collective variables and divide it into stream tubes. Each tube contains a definite fraction of the total folding flow and can be associated with a certain pathway. Specifically, three temperatures were considered, T = 285K, T = 315K, and T = 325K. We have found that as the temperature increases, the contribution of pathway I, which is approximately 90% of the total folding flow at T = 285K, decreases to approximately 10% at T = 325K, i.e., pathway II becomes dominant. At T = 315K, both pathways contribute approximately equally. All these temperatures are found below the calculated melting point, which suggests that the Trp-cage folding mechanism is determined by kinetic factors rather than thermodynamics.
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Affiliation(s)
- Vladimir A Andryushchenko
- Institute of Thermophysics, SB RAS, 630090, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090, Novosibirsk, Russia.
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia.
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33
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Zuev YF, Litvinov RI, Sitnitsky AE, Idiyatullin BZ, Bakirova DR, Galanakis DK, Zhmurov A, Barsegov V, Weisel JW. Conformational Flexibility and Self-Association of Fibrinogen in Concentrated Solutions. J Phys Chem B 2017; 121:7833-7843. [DOI: 10.1021/acs.jpcb.7b05654] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russian Federation
- Kazan Federal University, 420000 Kazan, Russian Federation
| | - Rustem I. Litvinov
- Kazan Federal University, 420000 Kazan, Russian Federation
- Perelman
School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Bulat Z. Idiyatullin
- Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russian Federation
| | | | - Dennis K. Galanakis
- SUNY at Stony Brook School of Medicine, Stony Brook, New York 11794, United States
| | - Artem Zhmurov
- Moscow Institute of Physics & Technology, 141701 Moscow Region, Russian Federation
| | - Valeri Barsegov
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
- Moscow Institute of Physics & Technology, 141701 Moscow Region, Russian Federation
| | - John W. Weisel
- Perelman
School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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34
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Lomonosova E, Daw J, Garimallaprabhakaran AK, Agyemang NB, Ashani Y, Murelli RP, Tavis JE. Efficacy and cytotoxicity in cell culture of novel α-hydroxytropolone inhibitors of hepatitis B virus ribonuclease H. Antiviral Res 2017. [PMID: 28633989 DOI: 10.1016/j.antiviral.2017.06.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic Hepatitis B virus (HBV) infection is a major worldwide public health problem. Current direct-acting anti-HBV drugs target the HBV DNA polymerase activity, but the equally essential viral ribonuclease H (RNaseH) activity is unexploited as a drug target. Previously, we reported that α-hydroxytropolone compounds can inhibit the HBV RNaseH and block viral replication. Subsequently, we found that our biochemical RNaseH assay underreports efficacy of the α-hydroxytropolones against HBV replication. Therefore, we conducted a structure-activity analysis of 59 troponoids against HBV replication in cell culture. These studies revealed that antiviral efficacy is diminished by larger substitutions on the tropolone ring, identified key components in the substitutions needed for high efficacy, and revealed that cytotoxicity correlates with increased lipophilicity of the α-hydroxytropolones. These data provide key guidance for further optimization of the α-hydroxytropolone scaffold as novel HBV RNaseH inhibitors.
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Affiliation(s)
- Elena Lomonosova
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA; Saint Louis University Liver Center, Saint Louis, MO, USA
| | - Jil Daw
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | | | - Nana B Agyemang
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA
| | - Yashkumar Ashani
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA; PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA; Saint Louis University Liver Center, Saint Louis, MO, USA.
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35
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Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, Im W. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 2017; 38:1114-1124. [PMID: 27862047 PMCID: PMC5403596 DOI: 10.1002/jcc.24660] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, Illinois
| | - Xi Cheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Jumin Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Sang-Jun Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Kyu Il Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Hui Sun Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Jeffrey B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland
| | - Yifei Qi
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
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36
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Jia Z, Ackroyd C, Han T, Agrawal V, Liu Y, Christensen K, Dominy B. Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study. J Comput Chem 2017; 38:1183-1190. [PMID: 28437008 DOI: 10.1002/jcc.24768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/08/2017] [Accepted: 01/14/2017] [Indexed: 11/09/2022]
Abstract
One of the anthrax receptors, tumor endothelial marker 8 (TEM8), is reported to be a potential anticancer target due to its over-expression during tumor angiogenesis. To extend our BioLayer Interferometry study in PA-TEM8 binding, we present a computational approach to reveal the role of an integral metal ion on receptor structure and binding thermodynamics. We estimated the interaction energy between PA and TEM8 using computer simulation. Consistent with experimental study, computational results indicate the metal ion in TEM8 contributes significantly to the binding affinity, and PA-TEM8 binding is more favorable in the presence of Mg2+ than Ca2+ . Further, computational analysis suggests that the differences in PA-TEM8 binding affinity are comparable to the closely related integrin proteins. The conformation change, which linked to changes in activity of integrins, was not found in TEM8. In the present of Mg2+ , TEM8 remains in a conformation analogous to an integrin open (high-affinity) conformation. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhe Jia
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Christine Ackroyd
- Department of Chemistry and Biochemistry, C205 BNSN, Brigham Young University, Provo, Utah, 84602
| | - Tingting Han
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Vibhor Agrawal
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Yinling Liu
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Kenneth Christensen
- Department of Chemistry and Biochemistry, C205 BNSN, Brigham Young University, Provo, Utah, 84602
| | - Brian Dominy
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
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37
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Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates. J Mol Graph Model 2017; 73:179-190. [DOI: 10.1016/j.jmgm.2017.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/19/2017] [Accepted: 02/17/2017] [Indexed: 11/18/2022]
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38
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Steckmann T, Bhandari YR, Chapagain PP, Gerstman BS. Cooperative structural transitions in amyloid-like aggregation. J Chem Phys 2017; 146:135103. [DOI: 10.1063/1.4979516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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39
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Kononova O, Litvinov RI, Blokhin DS, Klochkov VV, Weisel JW, Bennett JS, Barsegov V. Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3. Biochemistry 2017; 56:1932-1942. [PMID: 28277676 DOI: 10.1021/acs.biochem.6b01113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Binding of soluble fibrinogen to the activated conformation of the integrin αIIbβ3 is required for platelet aggregation and is mediated exclusively by the C-terminal AGDV-containing dodecapeptide (γC-12) sequence of the fibrinogen γ chain. However, peptides containing the Arg-Gly-Asp (RGD) sequences located in two places in the fibrinogen Aα chain inhibit soluble fibrinogen binding to αIIbβ3 and make substantial contributions to αIIbβ3 binding when fibrinogen is immobilized and when it is converted to fibrin. Here, we employed optical trap-based nanomechanical measurements and computational molecular modeling to determine the kinetics, energetics, and structural details of cyclic RGDFK (cRGDFK) and γC-12 binding to αIIbβ3. Docking analysis revealed that NMR-determined solution structures of cRGDFK and γC-12 bind to both the open and closed αIIbβ3 conformers at the interface between the αIIb β-propeller domain and the β3 βI domain. The nanomechanical measurements revealed that cRGDFK binds to αIIbβ3 at least as tightly as γC-12. A subsequent analysis of molecular force profiles and the number of peptide-αIIbβ3 binding contacts revealed that both peptides form stable bimolecular complexes with αIIbβ3 that dissociate in the 60-120 pN range. The Gibbs free energy profiles of the αIIbβ3-peptide complexes revealed that the overall stability of the αIIbβ3-cRGDFK complex was comparable with that of the αIIbβ3-γC-12 complex. Thus, these results provide a mechanistic explanation for previous observations that RGD- and AGDV-containing peptides are both potent inhibitors of the αIIbβ3-fibrinogen interactions and are consistent with the observation that RGD motifs, in addition to AGDV, support interaction of αIIbβ3 with immobilized fibrinogen and fibrin.
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Affiliation(s)
- Olga Kononova
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States.,Moscow Institute of Physics and Technology , Moscow Region 141700, Russian Federation
| | | | | | | | | | | | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States.,Moscow Institute of Physics and Technology , Moscow Region 141700, Russian Federation
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40
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Jia Z, Beugelsdijk A, Chen J, Schmit JD. The Levinthal Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space. J Phys Chem B 2017; 121:1576-1586. [PMID: 28129689 DOI: 10.1021/acs.jpcb.7b00253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The formation of amyloid fibrils has been associated with many neurodegenerative disorders, yet the mechanism of aggregation remains elusive, partly because aggregation time scales are too long to probe with atomistic simulations. A microscopic theory of fibril elongation was recently developed that could recapitulate experimental results with respect to the effects of temperature, denaturants, and protein concentration on fibril growth kinetics (Schmit, J. D. J. Chem. Phys. 2013, 138 (18), 185102). The theory identifies the conformational search over H-bonding states as the slowest step in the aggregation process and suggests that this search can be efficiently modeled as a random walk on a rugged one-dimensional energy landscape. This insight motivated the multiscale computational algorithm for simulating fibril growth presented in this paper. Briefly, a large number of short atomistic simulations are performed to compute the system diffusion tensor in the reaction coordinate space predicted by the analytic theory. Ensemble aggregation pathways and growth kinetics are then computed from Markov state model (MSM) trajectories. The algorithm is deployed here to understand the fibril growth mechanism and kinetics of Aβ16-22 and three of its mutants. The order of growth rates of the wild-type and two single mutation peptides (CHA19 and CHA20) predicted by the MSM trajectories is consistent with experimental results. The simulation also correctly predicts that the double mutation (CHA19/CHA20) would reduce the fibril growth rate, even though the degree of rate reduction with respect to either single mutation is overestimated. This artifact may be attributed to the simplistic implicit solvent model. These trends in the growth rate are not apparent from inspection of the rate constants of individual bonds or the lifetimes of the mis-registered states that are the primary kinetic traps but only emerge in the ensemble of trajectories generated by the MSM.
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Affiliation(s)
- Zhiguang Jia
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Alex Beugelsdijk
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Jeremy D Schmit
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
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41
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Dutagaci B, Sayadi M, Feig M. Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices. J Comput Chem 2017; 38:1308-1320. [PMID: 28160300 DOI: 10.1002/jcc.24691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/18/2016] [Accepted: 11/17/2016] [Indexed: 11/07/2022]
Abstract
The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) by combining separate contributions from each of the membrane components. The HDGBvdW model is validated with a series of test cases ranging from membrane insertion and pair association profiles of amino acid side chain analogs and transmembrane helices. Overall, the HDGBvdW model leads to increased agreement with explicit membrane simulation results and experimental data. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
| | - Maryam Sayadi
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
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Kumar A, Ranbhor R, Patel K, Ramakrishnan V, Durani S. Automated protein design: Landmarks and operational principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 125:24-35. [PMID: 27979438 DOI: 10.1016/j.pbiomolbio.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022]
Abstract
Protein design has an eventful history spanning over three decades, with handful of success stories reported, and numerous failures not reported. Design practices have benefited tremendously from improvements in computer hardware and advances in scientific algorithms. Though protein folding problem still remains unsolved, the possibility of having multiple sequence solutions for a single fold makes protein design a more tractable problem than protein folding. One of the most significant advancement in this area is the implementation of automated design algorithms on pre-defined templates or completely new folds, optimized through deterministic and heuristic search algorithms. This progress report provides a succinct presentation of important landmarks in automated design attempts, followed by brief account of operational principles in automated design methods.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, ON, M5S3H6, Canada.
| | | | | | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India.
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology, Bombay, 400076, India
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Harrison ET, Weidner T, Castner DG, Interlandi G. Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations. Biointerphases 2016; 12:02D401. [PMID: 27923271 PMCID: PMC5148762 DOI: 10.1116/1.4971381] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/06/2016] [Accepted: 11/18/2016] [Indexed: 01/17/2023] Open
Abstract
A Monte Carlo algorithm was developed to predict the most likely orientations of protein G B1, an immunoglobulin G (IgG) antibody-binding domain of protein G, adsorbed onto a hydrophobic surface. At each Monte Carlo step, the protein was rotated and translated as a rigid body. The assumption about rigidity was supported by quartz crystal microbalance with dissipation monitoring experiments, which indicated that protein G B1 adsorbed on a polystyrene surface with its native structure conserved and showed that its IgG antibody-binding activity was retained. The Monte Carlo simulations predicted that protein G B1 is likely adsorbed onto a hydrophobic surface in two different orientations, characterized as two mutually exclusive sets of amino acids contacting the surface. This was consistent with sum frequency generation (SFG) vibrational spectroscopy results. In fact, theoretical SFG spectra calculated from an equal combination of the two predicted orientations exhibited reasonable agreement with measured spectra of protein G B1 on polystyrene surfaces. Also, in explicit solvent molecular dynamics simulations, protein G B1 maintained its predicted orientation in three out of four runs. This work shows that using a Monte Carlo approach can provide an accurate estimate of a protein orientation on a hydrophobic surface, which complements experimental surface analysis techniques and provides an initial system to study the interaction between a protein and a surface in molecular dynamics simulations.
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Affiliation(s)
- Elisa T Harrison
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark and Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David G Castner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 and Department of Bioengineering, University of Washington, Seattle, Washington 98195
| | - Gianluca Interlandi
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
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44
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Perkins SJ, Wright DW, Zhang H, Brookes EH, Chen J, Irving TC, Krueger S, Barlow DJ, Edler KJ, Scott DJ, Terrill NJ, King SM, Butler PD, Curtis JE. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). J Appl Crystallogr 2016; 49:1861-1875. [PMID: 27980506 PMCID: PMC5139988 DOI: 10.1107/s160057671601517x] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.
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Affiliation(s)
- Stephen J. Perkins
- Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - David W. Wright
- Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Hailiang Zhang
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - Emre H. Brookes
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Thomas C. Irving
- Department of Biology, Illinois Institute of Technology, 3101 S. Dearborn, Chicago, IL 60616, USA
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - David J. Barlow
- Pharmacy Department, Franklin-Wilkins Building, King’s College London, 150 Stamford Street, London SE1 9NH, UK
| | - Karen J. Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0FA, UK
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - Nicholas J. Terrill
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK
| | - Stephen M. King
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - Paul D. Butler
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
- Department of Chemistry, The University of Tennessee, Knoxville, TN 37996-1600, USA
| | - Joseph E. Curtis
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
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45
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Chuchuen O, Maher JR, Simons MG, Peters JJ, Wax AP, Katz DF. Label-Free Measurements of Tenofovir Diffusion Coefficients in a Microbicide Gel Using Raman Spectroscopy. J Pharm Sci 2016; 106:639-644. [PMID: 27837968 DOI: 10.1016/j.xphs.2016.09.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 09/11/2016] [Accepted: 09/21/2016] [Indexed: 02/05/2023]
Abstract
Confocal Raman spectroscopy was implemented in a new label-free technique to quantify molecular diffusion coefficients within gels. A leading anti-HIV drug, tenofovir, was analyzed in a clinical microbicide gel. The gel was tested undiluted, and in 10%-50% wt/wt dilutions with vaginal fluid simulant to capture the range of conditions likely occurring in vivo. The concentration distributions of tenofovir in gel over time and space were measured and input to a mathematical diffusion model to deduce diffusion coefficients. These were 3.16 ± 0.11 × 10-6 cm2/s in undiluted gel, and increased by 11%-46% depending on the extent of dilution. Results were interpreted with respect to traditional release rate measurements in devices such as Franz cells. This comparison highlighted an advantage of our assay in that it characterizes the diffusive barrier within the gel material itself; in contrast, release rate in the traditional assay is affected by external conditions, such as drug partitioning at the gel/liquid sink interface. This new assay is relevant to diffusion in polymeric hydrogels over pharmacologically relevant length scales, for example, those characteristic of topical drug delivery. Resulting transport parameters are salient measures of drug delivery potential, and serve as inputs to computational models of drug delivery performance.
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Affiliation(s)
- Oranat Chuchuen
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Jason R Maher
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Morgan G Simons
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Jennifer J Peters
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Adam P Wax
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - David F Katz
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708; Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina 27708.
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Goubko M, Miloserdov O, Yampolskii Y, Alentiev A, Ryzhikh V. A novel model to predict infinite dilution solubility coefficients in glassy polymers. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/polb.24263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mikhail Goubko
- V. A. Trapeznikov Institute of Control Sciences of Russian Academy of Sciences; 65 Profsoyuznaya street Moscow 117997 Russia
| | - Oleg Miloserdov
- V. A. Trapeznikov Institute of Control Sciences of Russian Academy of Sciences; 65 Profsoyuznaya street Moscow 117997 Russia
| | - Yuri Yampolskii
- A.V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences; 29 Leninsky prospect Moscow 119991 Russia
| | - Alexander Alentiev
- A.V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences; 29 Leninsky prospect Moscow 119991 Russia
| | - Victoria Ryzhikh
- A.V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences; 29 Leninsky prospect Moscow 119991 Russia
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47
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Bodmer NK, Theisen KE, Dima RI. Molecular investigations into the mechanics of a muscle anchoring complex. Biophys J 2016; 108:2322-32. [PMID: 25954889 DOI: 10.1016/j.bpj.2015.03.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/16/2015] [Accepted: 03/13/2015] [Indexed: 11/15/2022] Open
Abstract
The titin-telethonin complex, essential for anchoring filaments in the Z-disk of the sarcomere, is composed of immunoglobulin domains. Surprisingly, atomic force microscopy experiments showed that it resists forces much higher than the typical immunoglobulin domain and that the force distribution is unusually broad. To investigate the origin of this behavior, we developed a multiscale simulation approach, combining minimalist and atomistic models (SOP-AT). By following the mechanical response of the complex on experimental timescales, we found that the mechanical stability of titin-telethonin is modulated primarily by the strength of contacts between telethonin and the two titin chains, and secondarily by the timescales of conformational excursions inside telethonin and the pulled titin domains. Importantly, the conformational transitions executed by telethonin in simulations support its proposed role in mechanosensing. Our SOP-AT computational approach thus provides a powerful tool for the exploration of the link between conformational diversity and the broadness of the mechanical response, which can be applied to other multidomain complexes.
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Affiliation(s)
| | - Kelly E Theisen
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio.
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48
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Kyrychenko A. NANOGOLD decorated by pHLIP peptide: comparative force field study. Phys Chem Chem Phys 2016; 17:12648-60. [PMID: 25903421 DOI: 10.1039/c5cp01136a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP.
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Affiliation(s)
- A Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody square, Kharkiv 61022, Ukraine.
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49
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Hua DP, Huang H, Roy A, Post CB. Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents. Protein Sci 2016; 25:204-18. [PMID: 26189497 PMCID: PMC4815311 DOI: 10.1002/pro.2753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/15/2015] [Indexed: 11/11/2022]
Abstract
Three implicit solvent models, namely GBMVII, FACTS, and SCPISM, were evaluated for their abilities to emulate an explicit solvent environment by comparing the simulated conformational ensembles, dynamics, and electrostatic interactions of the Src SH2 domain and the Lyn kinase domain. This assessment in terms of structural features in folded proteins expands upon the use of hydration energy as a metric for comparison. All-against-all rms coordinate deviation, average positional fluctuations, and ion-pair distance distribution were used to compare the implicit solvent models with the TIP3P explicit solvent model. Our study shows that the Src SH2 domains solvated with TIP3P, GBMVII, and FACTS sample similar global conformations. Additionally, the Src SH2 ion-pair distance distributions of solvent-exposed side chains corresponding to TIP3P, GBMVII, and FACTS do not differ substantially, indicating that GBMVII and FACTS are capable of modeling these electrostatic interactions. The ion-pair distance distributions of SCPISM are distinct from others, demonstrating that these electrostatic interactions are not adequately reproduced with the SCPISM model. On the other hand, for the Lyn kinase domain, a non-globular protein with bilobal structure and a large concavity on the surface, implicit solvent does not accurately model solvation to faithfully reproduce partially buried electrostatic interactions and lobe-lobe conformations. Our work reveals that local structure and dynamics of small, globular proteins are modeled well using FACTS and GBMVII. Nonetheless, global conformations and electrostatic interactions in concavities of multi-lobal proteins resulting from simulations with implicit solvent models do not match those obtained from explicit water simulations.
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Affiliation(s)
- Duy P Hua
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - He Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - Amitava Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
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50
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Ceres N, Lavery R. Improving the treatment of coarse-grain electrostatics: CVCEL. J Chem Phys 2015; 143:243118. [DOI: 10.1063/1.4933434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- N. Ceres
- Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367, France
| | - R. Lavery
- Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367, France
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